Variant report

Variant	rs2298060
Chromosome Location	chr6:24426822-24426823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24426316..24427953-chr6:24428203..24431025,2	MCF-7	breast:
2	chr6:24426425..24428903-chr6:24718888..24721058,2	MCF-7	breast:
3	chr6:24424501..24427723-chr6:24493880..24496586,3	MCF-7	breast:
4	chr6:24421603..24423406-chr6:24425758..24427352,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000112294	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1054862	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054868	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133526	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889240	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889242	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889253	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16901722	0.91[ASN][1000 genomes]
rs17306130	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273606	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298059	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3469	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747771	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747772	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818936	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827641	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271775	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271781	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45448393	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45478094	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45482500	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45574139	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45590133	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461006	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3331318	chr6:24426499-24426891	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2298060	GPLD1	cis	Esophagus Muscularis	GTEx
rs2298060	MRS2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24404600-24437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24405000-24427600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:24405400-24427000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:24405400-24427200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:24405400-24427200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:24405400-24427600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:24405400-24427600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:24405400-24428200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:24406000-24427000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:24406400-24427600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:24406600-24427400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:24407400-24427200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:24407600-24427000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr6:24407600-24427600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr6:24407600-24428200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr6:24407800-24427600	Strong transcription	Fetal Thymus	thymus
17	chr6:24408000-24427800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:24409000-24427000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:24409200-24427600	Strong transcription	Dnd41	blood
20	chr6:24410000-24430800	Strong transcription	Left Ventricle	heart
21	chr6:24412200-24427600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:24412200-24427600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:24412200-24427600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr6:24412200-24427600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:24412200-24428200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:24412400-24427200	Strong transcription	K562	blood
27	chr6:24412400-24427600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:24412400-24427600	Strong transcription	Fetal Brain Female	brain
29	chr6:24412600-24428600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:24412600-24429000	Strong transcription	Primary B cells from cord blood	blood
31	chr6:24412600-24430800	Strong transcription	Primary T cells from cord blood	blood
32	chr6:24412800-24427200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:24413400-24427800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:24413400-24429600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:24416600-24427600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr6:24417400-24427600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:24417400-24451800	Strong transcription	Liver	Liver
38	chr6:24419400-24427200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr6:24420000-24428200	Strong transcription	GM12878-XiMat	blood
40	chr6:24420600-24428800	Weak transcription	Stomach Mucosa	stomach
41	chr6:24420600-24429000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:24421200-24428600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:24421200-24428600	Weak transcription	Thymus	Thymus
44	chr6:24421200-24429000	Weak transcription	NHLF	lung
45	chr6:24421200-24448800	Weak transcription	Gastric	stomach
46	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
47	chr6:24421400-24434000	Weak transcription	Fetal Brain Male	brain
48	chr6:24421600-24427000	Weak transcription	Colonic Mucosa	Colon
49	chr6:24421600-24432000	Weak transcription	Fetal Heart	heart
50	chr6:24422400-24429400	Strong transcription	Brain Anterior Caudate	brain

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